You could think of lots of ways to protect your ship. Instead of water you could just put a really thick plate of steel in front of you or just about anything else. Of course, more weight means you need more fuel to get yourself moving so you endup in a vicious circle of more fuel needing a bigger ship to carry it thus needing a bigger (and heavier) shield to protect yourself so you need yet more fuel to move yourself and then a still bigger ship and so on.
Also, whether you use water or steel or whatever it will be eaten away as you travel…much the same as rocks are worn down over time by the constant pounding of waves. Sooner or later your shield, no matter how big, will have to be replaced. That is certainly possible to do (keep stopping at various solar systems to grab resources to build new shields) but it sure makes such travel a hassle (and you had better know beforehand that the solar system you’ll be stopping at actually has the resources you need or you’ll be stuck there).